To infect cells with a particular multiplicity of infection, it is essential to know the concentration of virus in the inoculum. Here we describe a highly reliable and controllable method for plaque purification using cell-repellent surfaces micropatterned on the substrate. Micropatterning of localized chemical or biochemical domains has the potential to become a powerful tool in controlling the seeding of cells. The cell array was reliably fabricated with micropatterned surfaces, and the number of cells in a pattern was easily controlled by the cell density in the media and micropattern size. The cell micropatterns were infected with baculoviruses to form an array of virus plaques. GFP-modified and wild-type baculoviruses were used to verify the feasibility of purifying a specific plaque. Using confocal microscopy, GFP-expressing plaques were readily selectable and removable.